Welcome to pyww3’s documentation!
pyww3
Python wrapper for NOAA’s WaveWatchIII (WW3) Model.
This package wraps around the WW3’s executables by properly defining the namelists (.nml) required to drive the model’s executables.
Requirements
pyww3 requires WaveWatchIII to be properly compiled with netCDF4 available in your $PATH.
Please follow the installation instructions from NOAA.
Programs supported: ww3_grid, ww3_prnc, ww3_shel, ww3_ounf, ww3_ounp and ww3_bounc.
Note that I don’t have plans to support programs that require ASCII input (such as ww3_outf) even tough they may have an associated namelist.
You will need python 3.7+ because of the extensive usage of dataclasses.
Getting Started
All the implemented classes have the same structure and methods. For example,
to run simulation with ww3_shel you do:
import datetime
from pyww3.shel import WW3Shel
W = WW3Shel(nproc=8,
runpath="tests/test_run/",
mod_def="tests/test_data/GLOB_60_MIN.ww3grid",
domain_start=datetime.datetime(2010, 1, 1, 0),
domain_stop=datetime.datetime(2010, 1, 1, 2),
input_forcing_winds=True,
input_forcing_ice_conc=True,
date_field_stride=3600,
date_point_stride=3600,
date_restart_stride=3600,
type_point_file="tests/test_data/boundary_point_list.txt")
W.to_file() # writes ww3_shel.nml in the run path
W.run() # run the simulation
print(W.stdout) # print the output given by WW3
Credits
This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.
WW3 is maintained and distributed by NOAA’s Environmental Modeling Center (EMC).
Disclaimer
There is no warranty for the program, to the extent permitted by applicable law except when otherwise stated in writing the copyright holders and/or other parties provide the program “as is” without warranty of any kind, either expressed or implied, including, but not limited to, the implied warranties of merchantability and fitness for a particular purpose. the entire risk as to the quality and performance of the program is with you. should the program prove defective, you assume the cost of all necessary servicing, repair or correction.
Installation
Stable release
To install pyww3, run this command in your terminal:
$ pip install pyww3
This is the preferred method to install pyww3, as it will always install the most recent stable release.
If you don’t have pip installed, this Python installation guide can guide you through the process.
From sources
The sources for pyww3 can be downloaded from the Github repo.
You can either clone the public repository:
$ git clone git://github.com/caiostringari/pyww3
Or download the tarball:
$ curl -OJL https://github.com/caiostringari/pyww3/tarball/master
Once you have a copy of the source, you can install it with:
$ python setup.py install
Usage
The main goal of pyww3 is programmatically to provide access to the
parameters that the user has to manually input the WW3 namelist files.
For example, if a namelist defines the following:
&SPECTRUM_NML
SPECTRUM%XFR = 1.1
SPECTRUM%FREQ1 = 0.04118
SPECTRUM%NK = 32
SPECTRUM%NTH = 24
/
You are able to write the same in python as:
spectrum_xfr: int = 1.1
spectrum_freq1: int = 0.04118
spectrum_nk: int = 32
spectrum_thoff: int = 0
All pyww3 classes use type hinting and all parameters are converted to the strings
that WW3 is expecting. Data validation is done in the __post_init__
method of each class. The checks include searching for required files and, for
some parameters, checking if the inputs are compatible to the namelist definitions.
All classes inherit from WW3Base. This class
implements the methods to_file() which writes the namelist text to file, run()
which runs a given program and update_text() which can be used to manipulate
the namelist text ad-hoc. Each class implements the method populate_namelist()
that generates the namelist text.
WW3Grid
Program used to create grids. Only regular spherical grids and unstructured meshes were tested.
Example:
from pyww3.grid import WW3Grid
# dictionary with grid information. This is normally read from a JSON file.
grid_info = {"grid_nml": "GLOB_60_MIN.nml",
"grid_name": "GLOB_60M",
"grid_type":"RECT",
"grid_coord":"SPHE",
"grid_clos": "NONE",
"rect_nx": 360,
"rect_ny": 157,
"rect_sx": 1.0,
"rect_sy": 1.0,
"rect_sf": 1.0,
"rect_x0": -180.0,
"rect_y0": -78.0,
"rect_sf0" :1.0,
"grid_zlim": -0.1,
"grid_dmin": 2.5,
"depth_filename": "GLOB_60_MIN.depth_ascii",
"depth_sf": 0.0010,
"obst_filename": "GLOB_60_MIN.obstr_lev1",
"obst_sf": 0.010,
"mask_filename": "GLOB_60_MIN.maskorig_ascii"}
# create the instance
W = WW3GRid(runpath="some/valid/path/",
grid_name=grid_info["grid_type"],
grid_nml=grid_info["grid_nml"],
grid_type=grid_info["grid_type"],
grid_coord=grid_info["grid_coord"],
grid_clos=grid_info["grid_clos"],
rect_nx=grid_info["rect_nx"],
rect_ny=grid_info["rect_ny"],
rect_sx=grid_info["rect_sx"],
rect_sy=grid_info["rect_sy"],
rect_sf=grid_info["rect_sf"],
rect_x0=grid_info["rect_x0"],
rect_y0=grid_info["rect_y0"],
rect_sf0=grid_info["rect_sf0"],
grid_zlim=grid_info["grid_zlim"],
grid_dmin=grid_info["grid_dmin"],
depth_filename=os.path.join(datapath, grid_info["depth_filename"]),
depth_sf=grid_info["depth_sf"],
obst_filename=os.path.join(datapath, grid_info["obst_filename"]),
obst_sf=grid_info["obst_sf"],
mask_filename=os.path.join(datapath, grid_info["mask_filename"]))
# update namelist blocks that could cause errors.
W.update_text("&SED_NML", action="remove")
W.update_text("&SLOPE_NML", action="remove")
W.update_text("&CURV_NML", action="remove")
W.update_text("&UNST_NML", action="remove")
# Update the timesteps. Don't forget to update the namelist text!
W.timesteps_dtmax = 480.0 * 3
W.timesteps_dtxy = 160.0 * 3
W.timesteps_dtkth = 240.0 * 3
W.timesteps_dtmin = 10.0 * 3
W.text = W.populate_namelist()
# write ww3_grid.namelist in the `runpath`.
W.to_file()
# run `ww3_grid` in the `runpath`.
W.run()
WW3Bounc
Program used to post-process spectral netcdf files generated with ww3_ounp.
Usually used to created boundary conditions to a nested simulation.
Example:
from pyww3.bounc import WW3Bounc
# create the instance
W = WW3Bounc(runpath="some/valid/path/",
mod_def="mod_def.ww3",
bound_file="somefile.nc")
# write ww3_bounc.namelist in the `runpath`.
W.to_file()
# run `ww3_bounc` in the `runpath`.
W.run()
History
0.1.4 (2021-09-01)
First release on PyPI.
0.1.0 (2021-08-25)
First more or less usable version.
Contributing
Contributions are welcome, and they are greatly appreciated! Every little bit helps, and credit will always be given.
You can contribute in many ways:
Types of Contributions
Report Bugs
Report bugs at https://github.com/caiostringari/pyww3/issues.
If you are reporting a bug, please include:
Your operating system name and version.
Any details about your local setup that might be helpful in troubleshooting.
Detailed steps to reproduce the bug.
Fix Bugs
Look through the GitHub issues for bugs. Anything tagged with “bug” and “help wanted” is open to whoever wants to implement it.
Implement Features
Look through the GitHub issues for features. Anything tagged with “enhancement” and “help wanted” is open to whoever wants to implement it.
Write Documentation
pyww3 could always use more documentation, whether as part of the official pyww3 docs, in docstrings, or even on the web in blog posts, articles, and such.
Submit Feedback
The best way to send feedback is to file an issue at https://github.com/caiostringari/pyww3/issues.
If you are proposing a feature:
Explain in detail how it would work.
Keep the scope as narrow as possible, to make it easier to implement.
Remember that this is a volunteer-driven project, and that contributions are welcome :)
Get Started!
Ready to contribute? Here’s how to set up pyww3 for local development.
Fork the pyww3 repo on GitHub.
Clone your fork locally:
$ git clone git@github.com:your_name_here/pyww3.git
Install your local copy into a virtualenv. Assuming you have virtualenvwrapper installed, this is how you set up your fork for local development:
$ mkvirtualenv pyww3 $ cd pyww3/ $ python setup.py developCreate a branch for local development:
$ git checkout -b name-of-your-bugfix-or-feature
Now you can make your changes locally.
When you’re done making changes, check that your changes pass flake8 and the tests, including testing other Python versions with tox:
$ flake8 pyww3 tests $ python setup.py test or pytest $ toxTo get flake8 and tox, just pip install them into your virtualenv.
Commit your changes and push your branch to GitHub:
$ git add . $ git commit -m "Your detailed description of your changes." $ git push origin name-of-your-bugfix-or-featureSubmit a pull request through the GitHub website.
Pull Request Guidelines
Before you submit a pull request, check that it meets these guidelines:
The pull request should include tests.
If the pull request adds functionality, the docs should be updated. Put your new functionality into a function with a docstring, and add the feature to the list in README.rst.
The pull request should work for Python 3.5, 3.6, 3.7 and 3.8, and for PyPy. Check https://travis-ci.com/caiostringari/pyww3/pull_requests and make sure that the tests pass for all supported Python versions.
Tips
To run a subset of tests:
$ pytest tests.test_pyww3
Deploying
A reminder for the maintainers on how to deploy. Make sure all your changes are committed (including an entry in HISTORY.rst). Then run:
$ bump2version patch # possible: major / minor / patch
$ git push
$ git push --tags
Travis will then deploy to PyPI if tests pass.
API
WW3Base
WW3Bounc
WW3Grid
- class pyww3.grid.WW3GRid(runpath: str, grid_name: str, grid_nml: str, grid_type: str, grid_coord: str, grid_clos: str, output: str = 'ww3_grid.nml', spectrum_xfr: int = 1.1, spectrum_freq1: int = 0.04118, spectrum_nk: int = 32, spectrum_nth: int = 24, spectrum_thoff: int = 0, run_fldry: bool = False, run_flcx: bool = True, run_flcy: bool = True, run_flcth: bool = True, run_flck: bool = True, run_flsou: bool = True, timesteps_dtmax: float = 480.0, timesteps_dtxy: float = 160.0, timesteps_dtkth: float = 240.0, timesteps_dtmin: float = 10.0, grid_zlim: float = 0.0, grid_dmin: float = 0.0, rect_nx: int = 0, rect_ny: int = 0, rect_sx: float = 0.0, rect_sy: float = 0.0, rect_sf: float = 1.0, rect_x0: float = 0.0, rect_y0: float = 0.0, rect_sf0: float = 1.0, curv_nx: int = 0, curv_ny: int = 0, curv_xcoord_sf: float = 1.0, curv_xcoord_off: float = 0.0, curv_xcoord_filename: str = '', curv_xcoord_idf: int = 21, curv_xcoord_idla: int = 1, curv_xcoord_idfm: int = 1, curv_xcoord_format: str = '(....)', curv_ycoord_sf: float = 1.0, curv_ycoord_off: float = 0.0, curv_ycoord_filename: str = '', curv_ycoord_idf: int = 22, curv_ycoord_idla: int = 1, curv_ycoord_idfm: int = 1, curv_ycoord_format: str = '(....)', unst_sf: float = 1.0, unst_filename: str = '', unst_idla: int = 20, unst_idfm: int = 1, unst_format: int = '(20f10.2)', unst_ugobcfile: str = '', depth_sf: float = 1.0, depth_filename: str = '', depth_idf: int = 50, depth_dla: int = 1, depth_dfm: int = 1, depth_format: str = '(....)', mask_filename: str = '', mask_idf: int = 60, mask_idla: int = 1, mask_idfm: int = 1, mask_format: str = '(....)', obst_sf: float = 1.0, obst_filename: str = '', obst_idf: int = 70, obst_idla: int = 1, obst_idfm: int = 1, obst_format: str = '(....)', slope_sf: float = 1.0, slope_filename: str = '', slope_idf: int = 80, slope_idla: int = 1, slope_idfm: int = 1, slope_format: str = '(....)', sed_sf: float = 1.0, sed_filename: str = '', sed_idfm: int = 1, sed_idla: int = 1, sed_format: str = '(....)')[source]
This class abstracts the program ww3_grid. It is an extension of the class
pyww3.ww3.WW3Base().
WW3Ounf
- class pyww3.ounp.WW3Ounp(runpath: str, mod_def: str, output: str = 'ww3_ounp.nml', ww3_pnt: str = 'out_pnt.ww3', point_timestart: datetime.datetime = datetime.datetime(1900, 1, 1, 0, 0), point_timestride: int = 0, point_timecount: int = 1000000000, point_timesplit: int = 6, point_list: str = 'all', point_samefile: bool = True, point_buffer: int = 150, point_type: int = 1, file_prefix: str = 'ww3.', file_netcdf: int = 4, spectra_output: int = 3, spectra_scale_fac: int = 1, spectra_output_fac: int = 0, param_output: int = 4, source_output: int = 4, source_scale_fac: int = 0, source_output_fac: int = 0, source_table_fac: int = 0, source_spectrum: bool = True, source_input: bool = True, source_interactions: bool = True, source_dissipation: bool = True, source_bottom: bool = True, source_ice: bool = True, source_total: bool = True)[source]
This class abstracts the program ww3_ounf. It is an extension of the class
pyww3.ww3.WW3Base().
WW3Ounp
- class pyww3.ounf.WW3Ounf(runpath: str, mod_def: str, ww3_grd: str = 'out_grd.ww3', output: str = 'ww3_ounf.nml', field_timestart: datetime.datetime = datetime.datetime(1900, 1, 1, 0, 0), field_timestride: int = 0, field_timecount: int = 1000000000, field_timesplit: int = 6, field_list: typing.List[str] = <factory>, field_samefile: bool = True, field_partition: typing.List[int] = <factory>, field_type: int = 3, file_prefix: str = 'ww3.', file_netcdf: int = 4, file_ix0: int = 1, file_ixn: int = 1000000000, file_iy0: int = 1, file_iyn: int = 1000000000, smc_type: int = 1, smc_sxo: int = 0, smc_exo: int = 0, smc_syo: int = 0, smc_eyo: int = 0, smc_celfac: int = 1, smc_noval: int = -999)[source]
This class abstracts the program ww3_ounf. It is an extension of the class
pyww3.ww3.WW3Base().
WW3Prnc
- class pyww3.prnc.WW3Prnc(runpath: str, mod_def: str, forcing_field: str, forcing_grid_latlon: bool, file_filename: str, file_longitude: str, file_latitude: str, file_var_1: str, output: str = 'ww3_prnc.nml', file_var_2: str = ' ', file_var_3: str = ' ', forcing_timestart: datetime.datetime = datetime.datetime(1900, 1, 1, 0, 0), forcing_timestop: datetime.datetime = datetime.datetime(2900, 12, 31, 0, 0), file_timeshift: str = '00000000 000000')[source]
This class abstracts the program ww3_prnc. It is an extension of the class
pyww3.ww3.WW3Base().
WW3Shel
Abstracts the ww3_shel program.
- class pyww3.shel.WW3Shel(runpath: str, mod_def: str, output: str = 'ww3_shel.nml', nproc: int = 1, domain_iostyp: int = 1, domain_start: datetime.datetime = datetime.datetime(1900, 1, 1, 0, 0), domain_stop: datetime.datetime = datetime.datetime(2900, 12, 31, 0, 0), input_forcing_water_levels: bool = False, input_forcing_currents: bool = False, input_forcing_winds: bool = False, input_forcing_ice_conc: bool = False, input_forcing_ice_param1: bool = False, input_forcing_ice_param2: bool = False, input_forcing_ice_param3: bool = False, input_forcing_ice_param4: bool = False, input_forcing_ice_param5: bool = False, input_forcing_mud_density: bool = False, input_forcing_mud_thickness: bool = False, input_forcing_mud_viscosity: bool = False, input_assim_mean: bool = False, input_assim_spec1d: bool = False, input_assim_spec2d: bool = False, type_field_list: typing.List[str] = <factory>, type_point_file: str = 'mylist', type_track_format: bool = True, type_partition_x0: int = 0, type_partition_xn: int = 0, type_partition_nx: int = 0, type_partition_y0: int = 0, type_partition_yn: int = 0, type_partition_ny: int = 0, type_coupling_sent: str = ' ', type_coupling_received: str = ' ', date_field_start: datetime.datetime = datetime.datetime(1900, 1, 1, 0, 0), date_field_stride: int = 0, date_field_stop: datetime.datetime = datetime.datetime(2900, 12, 31, 0, 0), date_point_start: datetime.datetime = datetime.datetime(1900, 1, 1, 0, 0), date_point_stride: int = 0, date_point_stop: datetime.datetime = datetime.datetime(2900, 12, 31, 0, 0), date_track_start: datetime.datetime = datetime.datetime(1900, 1, 1, 0, 0), date_track_stride: int = 0, date_track_stop: datetime.datetime = datetime.datetime(2900, 12, 31, 0, 0), date_restart_start: datetime.datetime = datetime.datetime(1900, 1, 1, 0, 0), date_restart_stride: int = 0, date_restart_stop: datetime.datetime = datetime.datetime(2900, 12, 31, 0, 0), date_boundary_start: datetime.datetime = datetime.datetime(1900, 1, 1, 0, 0), date_boundary_stride: int = 0, date_boundary_stop: datetime.datetime = datetime.datetime(2900, 12, 31, 0, 0), date_partition_start: datetime.datetime = datetime.datetime(1900, 1, 1, 0, 0), date_partition_stride: int = 0, date_partition_stop: datetime.datetime = datetime.datetime(2900, 12, 31, 0, 0), date_coupling_start: datetime.datetime = datetime.datetime(1900, 1, 1, 0, 0), date_coupling_stride: int = 0, date_coupling_stop: datetime.datetime = datetime.datetime(2900, 12, 31, 0, 0), date_restart: str = "'19000101 000000' '0' '29001231 000000'", homog_count_n_ic1: int = 0, homog_count_n_ic2: int = 0, homog_count_n_ic3: int = 0, homog_count_n_ic4: int = 0, homog_count_n_ic5: int = 0, homog_count_n_mdn: int = 0, homog_count_n_mth: int = 0, homog_count_n_mvs: int = 0, homog_count_n_lev: int = 0, homog_count_n_cur: int = 0, homog_count_n_wnd: int = 0, homog_count_n_ice: int = 0, homog_count_n_mov: int = 0, homog_input_1_name: str = 'unset', homog_input_1_date: datetime.datetime = datetime.datetime(1900, 1, 1, 0, 0), homog_input_1_value1: int = 0, homog_input_1_value2: int = 0, homog_input_1_value3: int = 0, homog_input_2_name: str = 'unset', homog_input_2_date: datetime.datetime = datetime.datetime(1900, 1, 1, 0, 0), homog_input_2_value1: int = 0, homog_input_2_value2: int = 0, homog_input_2_value3: int = 0, homog_input_3_name: str = 'unset', homog_input_3_date: datetime.datetime = datetime.datetime(1900, 1, 1, 0, 0), homog_input_3_value1: int = 0, homog_input_3_value2: int = 0, homog_input_3_value3: int = 0)[source]
This class abstracts the program ww3_ounf. It is an extension of the class
pyww3.ww3.WW3Base().